Alignment's a true pain for me since I don't have any Valve tracked equipment.
Do your real Vive controllers align to the in game Vive controllers?
I had to do some fakery to align things, but I matched up the controller models at the laser point in the menus. Basically the model aligns so that the Oculus model in SteamVR matches my Oculus Touch tracking.
I could try a second version with the orientation based on your comment and see if it feels right. Gotta rely entirely on feedback and that's a worrying scenario.